5 Bacterial genome statistics
genome_metadata <- read_tsv(file=str_c("data/",release,"_genome.tsv"))
assembly_metadata <- read_tsv(file=str_c("data/",release,"_assembly.tsv"))
host_metadata <- read_tsv(file=str_c("data/",release,"_host.tsv"))phylum_colors <- read_tsv("https://raw.githubusercontent.com/earthhologenome/EHI_taxonomy_colour/main/ehi_phylum_colors.tsv") %>%
right_join(genome_metadata, by=join_by(phylum == phylum)) %>%
select(phylum, colors) %>%
unique() %>%
arrange(phylum) %>%
pull(colors, name=phylum)5.2 Genome quality
genome_metadata %>%
summarise(completenes_mean=mean(completeness),
completenes_sd=sd(completeness),
contamination_mean=mean(contamination),
contamination_sd=sd(contamination)) %>%
tt()| completenes_mean | completenes_sd | contamination_mean | contamination_sd |
|---|---|---|---|
| 83.50943 | 15.27147 | 1.845634 | 2.074399 |
#Generate quality biplot
genome_biplot <- genome_metadata %>%
select(c(genome_id,domain,phylum,completeness,contamination,genome_size)) %>%
ggplot(aes(x=completeness,y=contamination,color=phylum)) +
geom_point(alpha=0.7, size=1) +
ylim(c(10,0)) +
scale_color_manual(values=phylum_colors) +
labs(y= "Contamination", x = "Completeness") +
theme_classic() +
theme(legend.position = "none")
#Generate contamination boxplot
genome_contamination <- genome_metadata %>%
ggplot(aes(y=contamination)) +
ylim(c(10,0)) +
geom_boxplot(colour = "#999999", fill="#cccccc") +
theme_void() +
theme(legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
plot.margin = unit(c(0, 0, 0.40, 0),"inches")) #add bottom-margin (top, right, bottom, left)
#Generate completeness boxplot
genome_completeness <- genome_metadata %>%
ggplot(aes(x=completeness)) +
xlim(c(50,100)) +
geom_boxplot(colour = "#999999", fill="#cccccc") +
theme_void() +
theme(legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
plot.margin = unit(c(0, 0, 0, 0.50),"inches")) #add left-margin (top, right, bottom, left)
#Render composite figure
grid.arrange(grobs = list(genome_completeness,genome_biplot,genome_contamination),
layout_matrix = rbind(c(1,1,1,1,1,1,1,1,1,1,1,4),
c(2,2,2,2,2,2,2,2,2,2,2,3),
c(2,2,2,2,2,2,2,2,2,2,2,3),
c(2,2,2,2,2,2,2,2,2,2,2,3),
c(2,2,2,2,2,2,2,2,2,2,2,3),
c(2,2,2,2,2,2,2,2,2,2,2,3),
c(2,2,2,2,2,2,2,2,2,2,2,3),
c(2,2,2,2,2,2,2,2,2,2,2,3),
c(2,2,2,2,2,2,2,2,2,2,2,3),
c(2,2,2,2,2,2,2,2,2,2,2,3),
c(2,2,2,2,2,2,2,2,2,2,2,3),
c(2,2,2,2,2,2,2,2,2,2,2,3)))5.3 Taxonomic statistics
#phylum
genome_metadata %>%
group_by(phylum) %>%
summarise(genomes=n(),
completenes=mean(completeness),
contamination=mean(contamination),
size=mean(genome_size)/1000000) %>%
arrange(-genomes) %>%
filter(phylum != "p__") %>%
tt()| phylum | genomes | completenes | contamination | size |
|---|---|---|---|---|
| p__Bacillota_A | 6029 | 83.66600 | 1.8519325 | 2.6764713 |
| p__Bacteroidota | 4301 | 82.61607 | 1.9322897 | 3.1244179 |
| p__Bacillota | 937 | 85.12057 | 2.0372423 | 1.9982295 |
| p__Pseudomonadota | 848 | 83.65697 | 1.7335684 | 2.2655061 |
| p__Desulfobacterota | 342 | 82.34488 | 1.4075263 | 2.7559354 |
| p__Verrucomicrobiota | 278 | 88.90504 | 0.8747950 | 2.4597815 |
| p__Bacillota_C | 217 | 87.40447 | 1.3593180 | 2.1676157 |
| p__Fusobacteriota | 215 | 79.36158 | 2.9872605 | 1.8014199 |
| p__Campylobacterota | 185 | 91.94984 | 0.5614054 | 1.6161529 |
| p__Cyanobacteriota | 131 | 84.78725 | 1.8406870 | 1.7740854 |
| p__Actinomycetota | 89 | 75.60730 | 2.4719775 | 1.9512960 |
| p__Bacillota_B | 66 | 79.31000 | 1.2919394 | 2.3504127 |
| p__Spirochaetota | 34 | 88.47882 | 0.7054706 | 1.9236368 |
| p__Deferribacterota | 32 | 84.84844 | 1.2626875 | 1.9807231 |
| p__Halobacteriota | 26 | 79.40154 | 0.9999231 | 1.5482744 |
| nan | 21 | 57.32810 | 6.5904762 | 2.2008697 |
| p__Elusimicrobiota | 19 | 83.18316 | 0.5752105 | 1.3912318 |
| p__Patescibacteria | 18 | 82.69833 | 2.1566667 | 0.7058587 |
| p__Synergistota | 16 | 84.26063 | 1.4668750 | 1.9546572 |
| p__Acidobacteriota | 4 | 81.94750 | 2.3075000 | 3.9519935 |
| p__Chlamydiota | 4 | 94.57250 | 0.4872500 | 1.1729767 |
| p__Chloroflexota | 4 | 67.88500 | 1.7650000 | 2.7801572 |
| p__Myxococcota | 3 | 75.54333 | 3.4300000 | 6.9908893 |
| p__Thermoplasmatota | 3 | 81.71667 | 0.6920000 | 1.2594070 |
| p__Methanobacteriota | 2 | 93.89000 | 0.1550000 | 1.9168890 |
| p__Bdellovibrionota | 1 | 96.59000 | 1.3200000 | 2.4054180 |
| p__Desulfobacterota_F | 1 | 99.99000 | 1.2000000 | 3.6243310 |
| p__Desulfobacterota_G | 1 | 81.00000 | 5.4100000 | 2.3275200 |
| p__Fibrobacterota | 1 | 76.19000 | 2.0900000 | 5.6243300 |
| p__J088 | 1 | 58.55000 | 7.3500000 | 2.1950540 |
| p__JAKLEM01 | 1 | 50.37000 | 2.7500000 | 1.5253600 |
| p__Nanoarchaeota | 1 | 90.32000 | 0.2600000 | 1.1657700 |
| p__Planctomycetota | 1 | 93.11000 | 1.7300000 | 4.3173220 |
#genus
genome_metadata %>%
group_by(genus) %>%
summarise(genomes=n(),
completenes=mean(completeness),
contamination=mean(contamination),
size=mean(genome_size)/1000000) %>%
arrange(-genomes) %>%
filter(genus != "g__") %>%
tt()| genus | genomes | completenes | contamination | size |
|---|---|---|---|---|
| g__Bacteroides | 782 | 78.33046 | 2.7439923 | 4.0009306 |
| g__Parabacteroides | 530 | 83.27357 | 1.9446698 | 4.0925221 |
| g__Odoribacter | 393 | 83.65000 | 1.8165903 | 3.2201619 |
| g__Phocaeicola | 376 | 81.57056 | 2.5304628 | 3.7949477 |
| g__Alistipes | 302 | 83.68404 | 2.5063113 | 2.3133999 |
| g__Mucinivorans | 298 | 85.13017 | 1.3451007 | 1.9634117 |
| g__Acetatifactor | 236 | 84.55886 | 2.0868475 | 3.1500363 |
| g__Prevotella | 169 | 82.46012 | 1.6331243 | 2.8287474 |
| g__Eisenbergiella | 166 | 85.81470 | 2.1805602 | 3.1225606 |
| g__JAAYNV01 | 166 | 90.83753 | 1.1252048 | 3.5637427 |
| g__Akkermansia | 156 | 90.83218 | 0.6747756 | 2.5919467 |
| g__CAG-95 | 148 | 88.17736 | 1.8279122 | 3.6271573 |
| g__Roseburia | 139 | 92.77223 | 2.0899424 | 3.6256912 |
| g__Alloprevotella | 110 | 84.58818 | 1.4283000 | 2.3205209 |
| g__Sutterella | 110 | 79.61727 | 2.4599182 | 1.9038248 |
| g__Parabacteroides_B | 109 | 85.93239 | 1.4079358 | 3.6262743 |
| g__Helicobacter_J | 108 | 94.49046 | 0.5139630 | 1.6525751 |
| g__JADFUS01 | 101 | 83.58069 | 1.7368317 | 1.9462928 |
| g__Fusobacterium_B | 99 | 78.06949 | 3.4891919 | 1.4979327 |
| g__Bilophila | 97 | 82.98887 | 1.2721340 | 2.9527382 |
| g__Faecalibacterium | 95 | 89.42579 | 1.4865579 | 2.3461926 |
| g__Ventrimonas | 92 | 85.84087 | 1.8352500 | 3.2875434 |
| g__CAG-485 | 89 | 82.15955 | 1.6241910 | 2.6924061 |
| g__Dielma | 88 | 84.93807 | 2.8190909 | 2.9218847 |
| g__UBA866 | 86 | 85.53233 | 0.6344070 | 2.2192333 |
| g__Anaerobiospirillum | 85 | 77.45506 | 1.7055294 | 2.8527684 |
| g__Faecousia | 85 | 83.13506 | 2.6253765 | 2.3809077 |
| g__Negativibacillus | 81 | 81.46185 | 1.4045556 | 2.6802667 |
| g__Hungatella_A | 80 | 80.82887 | 1.9934250 | 3.4562112 |
| g__Kineothrix | 80 | 89.97200 | 1.2764250 | 3.4972581 |
| g__Fusobacterium_A | 75 | 80.06187 | 2.6042800 | 2.1932724 |
| g__Rikenella | 75 | 81.77347 | 1.6146133 | 2.3120919 |
| g__Anaerotruncus | 73 | 78.51507 | 2.0466712 | 2.8334480 |
| g__Clostridium_Q | 71 | 81.96479 | 2.0313521 | 3.3676804 |
| g__Coproplasma | 69 | 87.66942 | 1.3636377 | 1.7947947 |
| g__Desulfovibrio | 69 | 82.01797 | 0.9959130 | 2.6519717 |
| g__MGBC136627 | 68 | 88.06206 | 1.7638235 | 3.5698897 |
| g__Mycoplasmoides | 67 | 93.36910 | 1.1217910 | 0.9221261 |
| g__Phascolarctobacterium_A | 66 | 92.03152 | 1.0318788 | 1.9133610 |
| g__Velocimicrobium | 64 | 81.50922 | 1.5529688 | 3.4432223 |
| g__Breznakia | 63 | 84.85667 | 2.5348730 | 2.3763616 |
| g__Enterocloster | 63 | 75.35508 | 2.0939683 | 3.5403101 |
| g__CAG-873 | 59 | 83.39458 | 1.1828814 | 2.2938315 |
| g__Duncaniella | 58 | 86.78741 | 1.4717586 | 2.8216755 |
| g__Blautia_A | 57 | 78.78474 | 2.5613509 | 2.7172184 |
| g__Mediterranea | 57 | 72.76281 | 1.9669825 | 2.5648671 |
| g__Blautia | 56 | 77.95143 | 2.0490893 | 2.3701946 |
| g__Gallimonas | 56 | 81.03089 | 1.7190179 | 1.5258936 |
| g__UBA3282 | 51 | 82.45765 | 2.5130588 | 2.8398454 |
| g__UBA7173 | 51 | 84.33098 | 1.3861569 | 2.3581050 |
| g__Paraprevotella | 49 | 82.23653 | 1.6722449 | 2.6908366 |
| g__Butyribacter | 48 | 86.93104 | 1.4707917 | 2.6354504 |
| g__Clostridium | 46 | 77.90761 | 3.6103913 | 2.8257833 |
| g__Mycoplasma_L | 45 | 82.54400 | 1.4944444 | 0.8095026 |
| g__Sarcina | 44 | 80.23545 | 3.5454773 | 2.6169732 |
| g__Tidjanibacter | 43 | 84.50977 | 1.2661860 | 1.8775005 |
| g__Fimenecus | 42 | 89.46048 | 0.8717619 | 1.9771575 |
| g__Lachnotalea | 42 | 89.20786 | 1.5045476 | 3.4696346 |
| g__Oscillibacter | 42 | 80.45357 | 1.8935476 | 2.4644769 |
| g__RGIG4733 | 42 | 87.44619 | 1.4109286 | 3.7190687 |
| g__Egerieousia | 41 | 85.61780 | 0.5395122 | 2.1987519 |
| g__Thomasclavelia | 41 | 85.09366 | 2.7437317 | 3.0183990 |
| g__COE1 | 40 | 83.61400 | 1.5067000 | 2.7887079 |
| g__Choladocola | 40 | 83.92400 | 2.7617250 | 2.9251094 |
| g__Dysosmobacter | 40 | 76.40050 | 4.1273500 | 2.1293909 |
| g__Lacrimispora | 40 | 84.73675 | 1.6506250 | 3.7337944 |
| g__Aeromonas | 38 | 82.06474 | 2.9341053 | 3.4772702 |
| g__UBA4293 | 38 | 90.73132 | 0.8545000 | 3.2863527 |
| g__Ruthenibacterium | 37 | 83.08595 | 1.4613784 | 2.3621107 |
| g__CAG-590 | 36 | 84.28139 | 2.1854167 | 2.9131451 |
| g__Intestinimonas | 36 | 67.58972 | 3.7120278 | 2.4002201 |
| g__JAGBWK01 | 36 | 88.61028 | 0.8640833 | 2.2896926 |
| g__Angelakisella | 35 | 82.57371 | 1.8402000 | 2.1102356 |
| g__CAG-269 | 34 | 76.29647 | 3.1020294 | 1.4356728 |
| g__MGBC140009 | 34 | 84.71118 | 2.3186176 | 3.7114479 |
| g__Mailhella | 34 | 78.87941 | 2.4362059 | 2.4408852 |
| g__CAZU01 | 33 | 79.14788 | 1.8684545 | 1.3614661 |
| g__Coprobacillus | 33 | 83.75333 | 1.8093939 | 3.0630959 |
| g__Gemmiger | 33 | 82.31758 | 1.4976061 | 2.3064288 |
| g__NHYM01 | 32 | 90.92844 | 0.4242187 | 1.4602849 |
| g__Anaeroplasma | 31 | 93.09806 | 0.9320968 | 1.8039064 |
| g__Escherichia | 31 | 84.29097 | 1.7174194 | 3.9955748 |
| g__Ventricola | 31 | 78.08355 | 2.3232581 | 2.3429855 |
| g__C-19 | 29 | 82.50138 | 2.4608621 | 3.1923226 |
| g__JALFVM01 | 29 | 80.08793 | 2.4764483 | 3.4476421 |
| g__Eubacterium_R | 28 | 82.10036 | 1.5371071 | 1.8415248 |
| g__Phascolarctobacterium | 28 | 90.41821 | 1.5412857 | 1.9465343 |
| g__RUG626 | 27 | 83.41259 | 2.4808519 | 2.1199066 |
| g__Schaedlerella | 27 | 76.37185 | 2.5315926 | 2.1058506 |
| g__Spyradosoma | 27 | 92.63148 | 0.8955185 | 2.0503313 |
| g__UMGS1251 | 26 | 83.22077 | 1.9021538 | 3.5291067 |
| g__14-2 | 25 | 90.15320 | 2.0857200 | 3.4587848 |
| g__Agathobacter | 25 | 88.42320 | 1.6148800 | 2.4598529 |
| g__CHH4-2 | 25 | 78.60160 | 2.2800400 | 3.3287936 |
| g__Choladousia | 25 | 77.94320 | 2.8195600 | 2.9779826 |
| g__Copromonas | 25 | 77.40440 | 2.2032000 | 2.9744614 |
| g__Hungatella | 25 | 70.40920 | 3.0590000 | 3.7537133 |
| g__Anaerotignum | 24 | 76.03750 | 0.9433750 | 1.8758788 |
| g__Coprococcus | 24 | 87.86208 | 1.8955000 | 2.3096639 |
| g__Eubacterium_F | 24 | 88.00542 | 1.3922917 | 2.3872639 |
| g__Hespellia | 24 | 90.11583 | 1.4644583 | 3.0224436 |
| g__Cryptobacteroides | 23 | 90.74261 | 0.9896522 | 2.2886778 |
| g__Fournierella | 23 | 73.29261 | 1.7945652 | 2.0709552 |
| g__Hydrogenoanaerobacterium | 23 | 82.05000 | 1.4367391 | 2.5756478 |
| g__Limiplasma | 23 | 85.40217 | 1.9344783 | 2.9201134 |
| g__Peptacetobacter | 23 | 66.78609 | 6.3539130 | 1.3394770 |
| g__Aphodousia | 22 | 79.60318 | 2.9750000 | 1.4761859 |
| g__CAJOIG01 | 22 | 80.08455 | 2.5090909 | 1.9237138 |
| g__UBA3402 | 22 | 79.38045 | 1.8536364 | 2.5131430 |
| g__UBA4292 | 22 | 86.04545 | 1.7050909 | 2.5733936 |
| g__Buttiauxella | 21 | 92.28000 | 2.7843810 | 4.3693456 |
| g__CALUXS01 | 21 | 93.35714 | 0.9500000 | 1.4981888 |
| g__Helicobacter_C | 21 | 85.56476 | 0.7808095 | 1.6630911 |
| g__MGBC165282 | 21 | 87.17952 | 1.6013333 | 3.7568950 |
| g__OM05-12 | 21 | 80.16048 | 1.3484286 | 2.6119786 |
| g__Onthomonas | 21 | 73.55238 | 3.7084762 | 1.8695060 |
| g__SZUA-378 | 21 | 86.10286 | 1.7407619 | 3.5192275 |
| nan | 21 | 57.32810 | 6.5904762 | 2.2008697 |
| g__Cetobacterium | 20 | 82.42600 | 2.2130000 | 1.7502279 |
| g__Collinsella | 20 | 68.50700 | 3.7920000 | 1.2146614 |
| g__Avoscillospira | 19 | 76.18842 | 2.6952632 | 2.0515814 |
| g__Brevinema | 19 | 87.14000 | 0.4433158 | 1.5556709 |
| g__Faecalimonas | 19 | 76.65263 | 2.3373684 | 1.9298566 |
| g__RGIG6463 | 19 | 81.38474 | 0.7295789 | 2.3652443 |
| g__Ligilactobacillus | 18 | 93.03889 | 1.4155556 | 2.0286136 |
| g__UBA3263 | 18 | 81.68278 | 0.7034444 | 1.7265587 |
| g__Caccovivens | 17 | 83.94176 | 1.1797647 | 1.0229758 |
| g__Enterenecus | 17 | 78.93353 | 2.6711765 | 2.9658340 |
| g__Lawsonibacter | 17 | 74.15353 | 2.4225294 | 2.0747672 |
| g__Malacoplasma | 17 | 88.28882 | 0.1523529 | 0.8257163 |
| g__Pelethenecus | 17 | 92.13941 | 1.6034118 | 1.6939882 |
| g__CAJLXD01 | 16 | 87.38875 | 1.7173750 | 1.6397237 |
| g__Lachnospira | 16 | 81.09125 | 2.1463125 | 2.2896428 |
| g__Limivicinus | 16 | 77.16688 | 1.9211875 | 2.0074292 |
| g__Methanimicrococcus | 16 | 81.64687 | 0.4523750 | 1.5468957 |
| g__Paramuribaculum | 16 | 84.08062 | 1.7264375 | 2.2698737 |
| g__RGIG8745 | 16 | 83.20250 | 1.8636875 | 3.2401001 |
| g__Scatousia | 16 | 81.75938 | 1.7710000 | 1.7558833 |
| g__Wujia | 16 | 92.33750 | 0.6005000 | 2.4458048 |
| g__Allobaculum | 15 | 80.32733 | 0.6946667 | 1.7607492 |
| g__CAJGBR01 | 15 | 94.39133 | 0.5913333 | 2.0574078 |
| g__Fimivivens | 15 | 74.84467 | 1.9449333 | 1.9233645 |
| g__Gabonibacter | 15 | 74.62867 | 1.7666667 | 1.5227652 |
| g__HGM05232 | 15 | 80.43800 | 0.7560000 | 2.4911500 |
| g__Hafnia | 15 | 97.14800 | 0.8912000 | 4.5309756 |
| g__JAAYQI01 | 15 | 70.40267 | 1.7640000 | 2.1705564 |
| g__JAIHAL01 | 15 | 86.08533 | 1.0728667 | 2.3547987 |
| g__MGBC143606 | 15 | 82.94867 | 1.4291333 | 2.5496931 |
| g__Megamonas | 15 | 86.81267 | 0.7893333 | 1.8396857 |
| g__RGIG3002 | 15 | 85.78133 | 1.7126000 | 3.0181283 |
| g__RGIG7193 | 15 | 84.87267 | 2.0974000 | 3.0412837 |
| g__Ruminococcus_D | 15 | 83.59733 | 1.7346667 | 2.5077879 |
| g__UBA7185 | 15 | 77.39200 | 2.4129333 | 3.0214479 |
| g__Enterobacter | 14 | 86.10786 | 2.5121429 | 4.1201701 |
| g__RGIG4057 | 14 | 81.93214 | 2.8901429 | 2.7730806 |
| g__Anaerorhabdus | 13 | 87.90846 | 2.2769231 | 1.9936744 |
| g__Intestinibacillus | 13 | 82.73154 | 1.7016154 | 2.3811686 |
| g__JAGNZR01 | 13 | 79.38538 | 2.4630769 | 1.9243046 |
| g__Limenecus | 13 | 85.33462 | 1.5905385 | 1.9508987 |
| g__Mobilisporobacter | 13 | 77.81462 | 1.0338462 | 3.3343508 |
| g__Pseudoflavonifractor | 13 | 73.34615 | 3.3313077 | 2.7327018 |
| g__Ruminococcus_B | 13 | 80.66154 | 2.4323077 | 2.1689964 |
| g__Scatacola_A | 13 | 94.56154 | 0.8500000 | 1.7181672 |
| g__Scatocola | 13 | 90.11923 | 1.0049231 | 1.5943258 |
| g__V9D3004 | 13 | 86.80923 | 0.4715385 | 2.0260051 |
| g__CAG-303 | 12 | 79.13333 | 0.9313333 | 2.1966957 |
| g__CAG-41 | 12 | 80.17250 | 1.8965833 | 2.0270892 |
| g__CAG-632 | 12 | 87.22250 | 1.1827500 | 2.6463514 |
| g__Lawsonia | 12 | 85.84250 | 0.1876667 | 1.6176053 |
| g__RUG115 | 12 | 94.12417 | 1.5739167 | 2.8114713 |
| g__Ruminococcus | 12 | 83.18250 | 1.3184167 | 2.2477094 |
| g__UBA1436 | 12 | 76.77083 | 0.5188333 | 1.2959140 |
| g__UMGS1601 | 12 | 86.77750 | 1.7325000 | 1.5879301 |
| g__WRDF01 | 12 | 77.01500 | 1.2186667 | 1.9408515 |
| g__Avidehalobacter | 11 | 82.76545 | 1.0967273 | 1.3185645 |
| g__Butyricicoccus | 11 | 78.50909 | 2.3300000 | 1.8126992 |
| g__CAG-115 | 11 | 86.46455 | 1.7650000 | 2.2535266 |
| g__CAG-353 | 11 | 79.36000 | 0.6951818 | 2.0303291 |
| g__CAG-475 | 11 | 92.92727 | 0.5990000 | 1.6750680 |
| g__Faecalibacillus | 11 | 81.96091 | 3.1748182 | 2.0685129 |
| g__HGM12587 | 11 | 78.72364 | 2.6268182 | 2.4847537 |
| g__JAGAJR01 | 11 | 87.12273 | 1.4683636 | 1.5099542 |
| g__JAJQCX01 | 11 | 93.42818 | 0.9560909 | 2.1504757 |
| g__Limisoma | 11 | 91.05000 | 0.8918182 | 2.2485101 |
| g__MGBC120314 | 11 | 85.83000 | 2.1864545 | 2.5837639 |
| g__MGBC124762 | 11 | 85.50091 | 1.8490909 | 1.6956766 |
| g__NSJ-61 | 11 | 82.36909 | 3.3135455 | 3.2853601 |
| g__Plesiomonas | 11 | 96.30909 | 0.9975455 | 3.0882576 |
| g__RUG762 | 11 | 83.39273 | 0.7753636 | 2.3945672 |
| g__Ruminococcus_E | 11 | 86.79636 | 1.4196364 | 1.8274238 |
| g__Scatovivens | 11 | 79.70909 | 4.3981818 | 1.5802639 |
| g__Turicibacter | 11 | 84.59909 | 2.8272727 | 2.4089091 |
| g__UBA1366 | 11 | 93.70545 | 0.1300000 | 2.4731303 |
| g__UBA3210 | 11 | 90.98455 | 1.1710909 | 1.6164445 |
| g__Vibrio | 11 | 85.75818 | 1.6739091 | 3.2846805 |
| g__Victivallis | 11 | 79.49636 | 2.2709091 | 1.9266078 |
| g__Anaerovorax | 10 | 74.51600 | 2.9513000 | 2.4406158 |
| g__Butyricimonas | 10 | 79.05000 | 1.9265000 | 3.5509095 |
| g__CAG-882 | 10 | 90.20700 | 1.5950000 | 2.5726870 |
| g__CALXXL01 | 10 | 79.31500 | 1.1430000 | 1.6799653 |
| g__Gallispira | 10 | 79.01400 | 0.8825000 | 1.7711217 |
| g__JAMPGF01 | 10 | 79.85800 | 1.6032000 | 1.9668257 |
| g__MGBC131033 | 10 | 82.75300 | 0.7994000 | 3.2036434 |
| g__Marvinbryantia | 10 | 79.79100 | 1.9050000 | 2.3818468 |
| g__Monoglobus | 10 | 78.41300 | 1.4600000 | 2.0817256 |
| g__Mucispirillum | 10 | 90.61400 | 0.9850000 | 2.1189145 |
| g__Phocaeicola_A | 10 | 76.59100 | 1.6730000 | 2.8213249 |
| g__RGIG8482 | 10 | 80.09400 | 1.5901000 | 1.4847350 |
| g__RUG11237 | 10 | 86.87400 | 2.9199000 | 3.2022827 |
| g__Scatenecus | 10 | 90.96700 | 0.8973000 | 1.7606572 |
| g__UBA2942 | 10 | 83.23500 | 1.0328000 | 2.5558953 |
| g__UBA7488 | 10 | 74.56400 | 2.1603000 | 1.2515580 |
| g__WRHT01 | 10 | 77.74800 | 0.9126000 | 2.5760728 |
| g__Amedibacillus | 9 | 77.57333 | 2.6465556 | 2.3740843 |
| g__CALWRD01 | 9 | 82.82222 | 1.0577778 | 1.9211042 |
| g__Citrobacter | 9 | 96.53444 | 1.4914444 | 4.9930733 |
| g__Coprovivens | 9 | 91.48000 | 3.2896667 | 1.6716806 |
| g__Emergencia | 9 | 83.66222 | 2.1676667 | 2.3280821 |
| g__Gallibacteroides | 9 | 84.24111 | 1.7688889 | 3.3193410 |
| g__Gastranaerophilus | 9 | 90.79000 | 1.2432222 | 1.7385116 |
| g__MGBC101980 | 9 | 85.99111 | 0.6412222 | 1.8073716 |
| g__Muribaculum | 9 | 94.57222 | 1.0854444 | 2.7427323 |
| g__RUG11200 | 9 | 90.18444 | 1.1166667 | 2.1175361 |
| g__Sphingobacterium | 9 | 85.83000 | 2.8977778 | 3.5378608 |
| g__Stoquefichus | 9 | 86.26889 | 1.2946667 | 2.8594062 |
| g__VSOB01 | 9 | 85.79667 | 1.9776667 | 2.2551070 |
| g__W0P33-017 | 9 | 75.43111 | 1.9594444 | 2.2320907 |
| g__Acinetobacter | 8 | 86.95500 | 2.3887500 | 2.8099321 |
| g__Anaerostipes | 8 | 95.33625 | 2.1637500 | 2.9547254 |
| g__Avirikenella | 8 | 85.40125 | 0.6075000 | 2.0423169 |
| g__CAG-103 | 8 | 85.61000 | 2.0267500 | 2.0896017 |
| g__CAG-345 | 8 | 83.67375 | 1.1837500 | 1.0782471 |
| g__CAG-411 | 8 | 83.07375 | 3.1503750 | 3.3120712 |
| g__CAG-826 | 8 | 78.53000 | 0.5166250 | 1.0761334 |
| g__CALURL01 | 8 | 75.55875 | 2.0738750 | 1.8507124 |
| g__Gallalistipes | 8 | 80.83375 | 2.7625000 | 2.1984795 |
| g__HGM11604 | 8 | 84.47875 | 2.7836250 | 2.1633904 |
| g__Paracoccus | 8 | 82.14750 | 3.6432500 | 3.4389716 |
| g__Parasutterella | 8 | 78.27500 | 1.8747500 | 2.0430726 |
| g__Pyramidobacter | 8 | 83.19500 | 1.4475000 | 1.8790534 |
| g__RF16 | 8 | 92.65000 | 0.9027500 | 2.2293974 |
| g__Ruminiclostridium_E | 8 | 95.08125 | 1.7415000 | 2.3879136 |
| g__UBA2882 | 8 | 96.81375 | 2.0061250 | 3.1634651 |
| g__UBA3855 | 8 | 85.68625 | 0.9150000 | 1.9672994 |
| g__UBA5026 | 8 | 71.98000 | 1.3760000 | 1.0391106 |
| g__UMGS27 | 8 | 85.86375 | 0.5930000 | 2.7725934 |
| g__Agathobaculum | 7 | 80.66429 | 1.2732857 | 1.8468374 |
| g__Aminipila | 7 | 65.84429 | 0.9242857 | 1.9814247 |
| g__Bifidobacterium | 7 | 77.75143 | 3.2428571 | 1.7703733 |
| g__Butyricicoccus_A | 7 | 83.87429 | 1.5264286 | 1.8705946 |
| g__CAG-1782 | 7 | 75.51286 | 0.8022857 | 1.6242547 |
| g__CAG-45 | 7 | 92.67714 | 2.2241429 | 2.7197579 |
| g__Campylobacter_D | 7 | 97.15571 | 0.4785714 | 1.6426069 |
| g__Enterousia | 7 | 83.04000 | 1.0925714 | 0.8671740 |
| g__Flavobacterium | 7 | 92.39000 | 0.5457143 | 2.4081123 |
| g__HGM11386 | 7 | 66.51286 | 0.9540000 | 1.9037451 |
| g__Klebsiella | 7 | 86.03286 | 2.2102857 | 4.7065624 |
| g__Lactococcus | 7 | 92.60429 | 0.2594286 | 2.0698919 |
| g__MGBC105563 | 7 | 81.80429 | 2.0500000 | 1.3936926 |
| g__MGBC116941 | 7 | 81.65000 | 0.8015714 | 1.6002653 |
| g__Merdiplasma | 7 | 84.17286 | 1.6585714 | 2.5816581 |
| g__Methanocorpusculum | 7 | 76.21000 | 1.1114286 | 1.4404811 |
| g__Nanosyncoccus | 7 | 78.73857 | 1.9728571 | 0.6424371 |
| g__QXXE01 | 7 | 84.92286 | 2.0905714 | 2.3193721 |
| g__Spyradomonas | 7 | 89.26571 | 2.0331429 | 1.9821764 |
| g__Streptococcus | 7 | 89.80429 | 0.7385714 | 1.6322636 |
| g__UBA2658 | 7 | 80.17714 | 0.9951429 | 1.8232519 |
| g__UMGS1663 | 7 | 72.89286 | 3.8432857 | 1.1852456 |
| g__WRKB01 | 7 | 70.70143 | 1.0100000 | 2.2559680 |
| g__Acutalibacter | 6 | 72.77833 | 3.3851667 | 2.0457885 |
| g__Aquirickettsiella | 6 | 92.20333 | 0.5300000 | 1.4524000 |
| g__Avilachnospira | 6 | 89.08833 | 2.0816667 | 1.9312978 |
| g__Bacteroides_G | 6 | 85.11167 | 1.1333333 | 2.8740010 |
| g__Budvicia | 6 | 97.23167 | 0.7200000 | 4.9492155 |
| g__CAAEEV01 | 6 | 76.04833 | 1.2863333 | 2.1261743 |
| g__CAG-267 | 6 | 85.30500 | 0.4736667 | 1.5094952 |
| g__CAG-56 | 6 | 74.37000 | 3.2266667 | 2.4492095 |
| g__CAG-603 | 6 | 77.86833 | 2.9916667 | 2.0778473 |
| g__CAJMNU01 | 6 | 80.00000 | 3.3713333 | 2.6483398 |
| g__CAKVBE01 | 6 | 93.98833 | 0.5483333 | 1.2549825 |
| g__CAMBRQ01 | 6 | 68.54667 | 2.5985000 | 2.1149285 |
| g__Caccovicinus | 6 | 79.73000 | 4.4755000 | 3.3505713 |
| g__Corynebacterium | 6 | 95.23500 | 0.6166667 | 2.9240602 |
| g__Craterilacuibacter | 6 | 78.19833 | 1.6433333 | 2.4728848 |
| g__Fimimonas | 6 | 94.67500 | 0.7883333 | 1.6774983 |
| g__Fimimorpha | 6 | 77.44333 | 2.1108333 | 2.6436418 |
| g__Fimivicinus | 6 | 90.49500 | 1.6315000 | 2.6179075 |
| g__Fimousia | 6 | 88.05000 | 3.7366667 | 2.9866347 |
| g__Galligastranaerophilus_A | 6 | 90.35167 | 1.2448333 | 1.8708660 |
| g__HGM11788 | 6 | 78.64500 | 1.7405000 | 1.9771743 |
| g__Helicobacter_A | 6 | 71.06333 | 1.1016667 | 1.6720998 |
| g__Lactobacillus | 6 | 77.14500 | 1.5933333 | 1.4695768 |
| g__Limadaptatus | 6 | 88.71167 | 0.7150000 | 1.5034233 |
| g__MGBC133411 | 6 | 91.97167 | 0.5825000 | 1.6246583 |
| g__Pelethomonas | 6 | 77.19333 | 2.8505000 | 1.7738373 |
| g__Phocea | 6 | 78.76000 | 0.3800000 | 2.3616727 |
| g__Pseudomonas_E | 6 | 73.11667 | 1.9236667 | 4.1134410 |
| g__RUG14156 | 6 | 76.58833 | 3.1843333 | 1.5746832 |
| g__SIG332 | 6 | 70.90667 | 1.1346667 | 2.8128192 |
| g__Staphylococcus | 6 | 77.58000 | 3.4650000 | 2.3945450 |
| g__Stercorousia | 6 | 93.04000 | 0.3431667 | 1.7025937 |
| g__UBA1213 | 6 | 78.93833 | 0.7800000 | 1.9680687 |
| g__UBA7050 | 6 | 77.24167 | 1.2411667 | 2.5507447 |
| g__UMGS1590 | 6 | 80.11500 | 1.3383333 | 1.5804592 |
| g__Ventrenecus | 6 | 72.16500 | 4.2231667 | 1.2198980 |
| g__Avimicrobium | 5 | 78.05800 | 3.3280000 | 1.3810848 |
| g__C-53 | 5 | 89.79600 | 1.9618000 | 2.6802446 |
| g__CAG-196 | 5 | 91.40600 | 2.6480000 | 1.8225938 |
| g__CAG-288 | 5 | 81.60200 | 2.7342000 | 1.3730546 |
| g__CAKSQF01 | 5 | 78.52200 | 1.3288000 | 2.0100842 |
| g__CALXRO01 | 5 | 75.59800 | 1.3176000 | 0.9162908 |
| g__Clostridium_AQ | 5 | 89.23400 | 1.3518000 | 3.7075122 |
| g__Dietzia | 5 | 65.72800 | 3.4980000 | 2.4245102 |
| g__Enterococcus_B | 5 | 83.77000 | 2.9840000 | 2.2895470 |
| g__Eubacterium_G | 5 | 90.79600 | 1.3840000 | 2.6178020 |
| g__Evtepia | 5 | 78.01800 | 2.3560000 | 2.0962234 |
| g__Faecimonas | 5 | 82.05400 | 3.5714000 | 1.3842976 |
| g__Faeciplasma | 5 | 93.68800 | 0.6060000 | 2.2825556 |
| g__Harryflintia | 5 | 80.60600 | 0.9074000 | 2.8972694 |
| g__Hepatoplasma | 5 | 90.49800 | 0.2704000 | 0.6231124 |
| g__Holdemanella | 5 | 80.62600 | 4.2340000 | 1.8072704 |
| g__JAFLUQ01 | 5 | 95.24400 | 1.2542000 | 1.9725872 |
| g__JAHHTP01 | 5 | 75.45400 | 0.8560000 | 2.0786310 |
| g__MGBC163490 | 5 | 77.85200 | 2.4320000 | 2.1987082 |
| g__Massiliimalia | 5 | 88.99200 | 0.5920000 | 2.1494490 |
| g__Onthocola_B | 5 | 84.46600 | 2.8500000 | 1.2800136 |
| g__Protoclostridium | 5 | 82.00800 | 1.5642000 | 1.8492688 |
| g__Pseudoruminococcus | 5 | 89.23200 | 2.0720000 | 1.8611478 |
| g__RGIG3040 | 5 | 97.39400 | 0.8642000 | 2.5891560 |
| g__RGIG6919 | 5 | 99.63000 | 0.9120000 | 2.6111662 |
| g__Romboutsia_C | 5 | 77.98200 | 3.2934000 | 2.1121234 |
| g__SIG299 | 5 | 83.56400 | 1.8448000 | 2.8279066 |
| g__UBA1224 | 5 | 85.63200 | 1.5040000 | 2.1756520 |
| g__UBA1794 | 5 | 84.96800 | 0.9356000 | 2.5147674 |
| g__UBA5578 | 5 | 90.46200 | 4.3400000 | 1.3501078 |
| g__UBA6857 | 5 | 74.29600 | 3.1540000 | 1.4470482 |
| g__UBA9732 | 5 | 91.61800 | 0.6700000 | 1.9234586 |
| g__Amedibacterium | 4 | 82.13750 | 2.3450000 | 2.0251692 |
| g__Aphodocola | 4 | 87.71250 | 1.7350000 | 1.1110805 |
| g__Avigastranaerophilus | 4 | 73.88250 | 3.2435000 | 1.6054120 |
| g__Butyrivibrio_A | 4 | 88.34250 | 0.7570000 | 1.9563928 |
| g__CAG-510 | 4 | 80.43500 | 0.9660000 | 2.3178183 |
| g__CAIPUE01 | 4 | 80.56500 | 0.4625000 | 1.5747565 |
| g__CAJTFG01 | 4 | 82.45500 | 3.5237500 | 1.7213820 |
| g__CAKRHR01 | 4 | 75.13750 | 0.7187500 | 1.5102438 |
| g__CALVGN01 | 4 | 82.83000 | 3.9250000 | 1.2572817 |
| g__Caccocola | 4 | 88.53500 | 0.9950000 | 1.9669778 |
| g__Coprobacter | 4 | 78.73750 | 1.2475000 | 2.7038865 |
| g__DTU064 | 4 | 86.46000 | 1.0125000 | 1.7178478 |
| g__Eubacterium_I | 4 | 71.91250 | 4.6975000 | 2.1710727 |
| g__Extibacter | 4 | 81.18250 | 2.3687500 | 3.1953317 |
| g__Harrysmithimonas | 4 | 87.94000 | 2.0750000 | 2.2354865 |
| g__Helicobacter_B | 4 | 88.63750 | 1.3825000 | 1.7077433 |
| g__IOR16 | 4 | 87.13750 | 0.9137500 | 2.2664415 |
| g__ISDg | 4 | 92.15750 | 1.0257500 | 2.2986802 |
| g__JAAWBF01 | 4 | 71.58750 | 2.9405000 | 2.2255128 |
| g__JAHHSE01 | 4 | 71.69750 | 3.3570000 | 1.6763702 |
| g__Lactonifactor | 4 | 85.68000 | 2.7100000 | 3.6724078 |
| g__Limosilactobacillus | 4 | 84.22500 | 3.0500000 | 1.7117478 |
| g__Luteimonas_D | 4 | 75.56500 | 2.4700000 | 2.1514993 |
| g__MGBC107952 | 4 | 70.80500 | 2.2402500 | 1.0953345 |
| g__MGBC114844 | 4 | 75.18750 | 1.3825000 | 2.5196693 |
| g__Merdicola | 4 | 77.20500 | 3.4107500 | 1.6477073 |
| g__Muricomes | 4 | 78.61750 | 3.4662500 | 4.4242112 |
| g__Oliverpabstia | 4 | 75.78750 | 2.1542500 | 2.8218315 |
| g__Pseudoscilispira | 4 | 69.95000 | 3.8690000 | 1.9631340 |
| g__RGIG1896 | 4 | 69.17000 | 0.4595000 | 1.8427130 |
| g__RGIG9287 | 4 | 76.25500 | 0.5290000 | 1.2484727 |
| g__SFTH01 | 4 | 64.97000 | 2.3650000 | 2.0539450 |
| g__Salmonella | 4 | 92.86500 | 2.2800000 | 4.5734605 |
| g__Scandinavium | 4 | 70.35000 | 5.0692500 | 3.4031733 |
| g__UBA5884 | 4 | 80.21250 | 0.4500000 | 2.0662410 |
| g__UBA6398 | 4 | 87.35000 | 1.3335000 | 2.3518997 |
| g__UBA7477 | 4 | 95.67000 | 0.5750000 | 2.1938167 |
| g__UBA940 | 4 | 66.11750 | 3.2475000 | 2.0416700 |
| g__UMGS1202 | 4 | 72.48000 | 2.8457500 | 2.1953048 |
| g__Ureaplasma | 4 | 91.80750 | 2.9627500 | 0.8600967 |
| g__Zag111 | 4 | 86.14250 | 2.4197500 | 1.7899070 |
| g__1XD42-69 | 3 | 71.61000 | 1.1433333 | 2.2772987 |
| g__Alistipes_A | 3 | 63.87333 | 0.6833333 | 1.4833253 |
| g__Anaerobiospirillum_A | 3 | 84.31000 | 0.5766667 | 2.1252407 |
| g__Anaerosphaera | 3 | 98.75333 | 0.9000000 | 1.6050477 |
| g__Bariatricus | 3 | 81.43000 | 1.8856667 | 3.0292130 |
| g__Brachybacterium | 3 | 64.48667 | 4.7233333 | 2.6186257 |
| g__CAG-266 | 3 | 99.85333 | 0.1966667 | 1.8609273 |
| g__CAG-452 | 3 | 76.11667 | 2.5300000 | 1.1779373 |
| g__CAG-465 | 3 | 74.60000 | 3.7193333 | 1.4152633 |
| g__CAG-977 | 3 | 82.86333 | 2.9430000 | 2.0519867 |
| g__CALXSC01 | 3 | 90.36667 | 1.1800000 | 1.4654037 |
| g__Caccenecus | 3 | 75.47667 | 4.2956667 | 1.0729603 |
| g__Catenibacterium | 3 | 88.83333 | 1.1033333 | 1.8893763 |
| g__Cryptoclostridium | 3 | 82.58667 | 0.7400000 | 1.6726777 |
| g__Eggerthella | 3 | 75.66667 | 1.9503333 | 2.6020303 |
| g__F23-B02 | 3 | 91.86333 | 0.5033333 | 1.8480567 |
| g__Faecalitalea | 3 | 81.71333 | 1.6866667 | 1.4002217 |
| g__Faecenecus | 3 | 86.95000 | 2.7866667 | 1.2110683 |
| g__Fimicola | 3 | 93.99000 | 0.7566667 | 2.2741243 |
| g__Helicobacter_G | 3 | 100.00000 | 0.0000000 | 1.5149717 |
| g__Howiella | 3 | 68.67000 | 0.4400000 | 1.5884423 |
| g__JAFLTL01 | 3 | 76.91000 | 2.5076667 | 2.0471750 |
| g__JAFUYI01 | 3 | 87.06000 | 0.8333333 | 1.3605633 |
| g__JAJQCF01 | 3 | 95.24000 | 0.1766667 | 1.9402947 |
| g__JALEPO01 | 3 | 83.35333 | 2.0266667 | 2.3942543 |
| g__Marseille-P3106 | 3 | 62.16667 | 4.4983333 | 1.6624623 |
| g__Merdenecus | 3 | 86.74000 | 2.7706667 | 2.2526657 |
| g__Merdimorpha | 3 | 80.58000 | 0.7300000 | 1.5979100 |
| g__Microbacterium | 3 | 83.60667 | 3.0493333 | 2.3846987 |
| g__Moheibacter | 3 | 97.86667 | 0.1933333 | 2.4978600 |
| g__Morganella | 3 | 97.21667 | 1.8966667 | 3.8163673 |
| g__Onthovivens | 3 | 88.70667 | 1.6066667 | 1.5028063 |
| g__Paenalcaligenes | 3 | 96.02000 | 1.4700000 | 2.3365020 |
| g__Paraclostridium | 3 | 82.09000 | 5.7133333 | 2.6121447 |
| g__Peptostreptococcus | 3 | 100.00000 | 0.4400000 | 2.1119113 |
| g__RGIG4140 | 3 | 83.61333 | 1.8100000 | 1.3726980 |
| g__RGIG6307 | 3 | 74.63667 | 3.1600000 | 2.5706307 |
| g__SIG200 | 3 | 84.60667 | 1.2033333 | 1.2456207 |
| g__SIG32 | 3 | 61.83000 | 5.4996667 | 1.4257573 |
| g__Scatavimonas | 3 | 94.25667 | 0.6403333 | 2.4870867 |
| g__Spiro-02 | 3 | 97.97000 | 1.6043333 | 3.6046057 |
| g__UBA1174 | 3 | 99.71000 | 0.2366667 | 1.6677177 |
| g__UBA11774 | 3 | 95.11000 | 1.5036667 | 2.7622537 |
| g__UBA11957 | 3 | 74.92667 | 3.6066667 | 2.7283987 |
| g__UBA1221 | 3 | 75.62667 | 2.0630000 | 1.7075177 |
| g__UBA1417 | 3 | 76.62667 | 2.2133333 | 1.9504873 |
| g__UBA4372 | 3 | 78.80667 | 0.7123333 | 2.2924333 |
| g__12844 | 2 | 79.00500 | 6.0600000 | 2.1416225 |
| g__Acaricomes | 2 | 83.10500 | 0.3850000 | 1.9028050 |
| g__Adamsella | 2 | 97.65500 | 2.4650000 | 2.0072200 |
| g__Avelusimicrobium | 2 | 82.78000 | 1.6265000 | 1.2236500 |
| g__Beduini | 2 | 84.23000 | 2.4380000 | 2.2955885 |
| g__Brachyspira | 2 | 61.97000 | 1.5700000 | 2.0049985 |
| g__Bullifex | 2 | 90.23500 | 0.8800000 | 2.2656315 |
| g__CAG-1031 | 2 | 91.04500 | 0.8350000 | 2.4178530 |
| g__CAG-273 | 2 | 89.40500 | 2.3500000 | 1.3872975 |
| g__CAG-449 | 2 | 96.87000 | 0.3200000 | 1.7364425 |
| g__CAG-492 | 2 | 75.24000 | 4.7050000 | 1.4435255 |
| g__CAG-552 | 2 | 71.13500 | 5.4550000 | 1.2167080 |
| g__CAIVKH01 | 2 | 72.66000 | 0.7850000 | 4.9133520 |
| g__CAJKWP01 | 2 | 67.99500 | 1.2455000 | 0.9406700 |
| g__CAKQDS01 | 2 | 95.05000 | 2.4215000 | 2.1544285 |
| g__CAKTEE01 | 2 | 91.24000 | 0.8500000 | 2.4502275 |
| g__CAKUFA01 | 2 | 60.76000 | 5.9550000 | 2.0217610 |
| g__CALTSX01 | 2 | 93.87500 | 0.8955000 | 1.2786980 |
| g__CALWPC01 | 2 | 78.11500 | 1.1110000 | 1.8187095 |
| g__CALXFK01 | 2 | 82.88000 | 1.0650000 | 1.8610855 |
| g__CCUG-7971 | 2 | 61.44500 | 7.9750000 | 2.0359945 |
| g__Catellicoccus | 2 | 81.70000 | 0.9850000 | 0.9953495 |
| g__Cellulosilyticum | 2 | 97.52000 | 2.9700000 | 3.8422710 |
| g__Cetobacterium_A | 2 | 92.11500 | 3.2800000 | 2.5676295 |
| g__Clostridium_H | 2 | 73.49000 | 7.8800000 | 1.2955745 |
| g__Clostridium_J | 2 | 71.68000 | 0.8250000 | 2.0860825 |
| g__Clostridium_N | 2 | 85.87000 | 1.4940000 | 1.9298470 |
| g__Copranaerobaculum | 2 | 86.36500 | 3.2515000 | 2.6776350 |
| g__DXYV01 | 2 | 69.56500 | 3.8600000 | 2.3761105 |
| g__Deefgea | 2 | 64.91000 | 2.1900000 | 1.8032995 |
| g__Dialister | 2 | 90.27000 | 1.0100000 | 2.1800845 |
| g__E4-60 | 2 | 84.33500 | 3.2300000 | 1.7521075 |
| g__Enterococcus | 2 | 89.61000 | 0.5100000 | 2.7818710 |
| g__Enterococcus_A | 2 | 51.88000 | 5.9160000 | 2.5312965 |
| g__Enterococcus_D | 2 | 91.22500 | 1.0255000 | 3.1736100 |
| g__FLUQ01 | 2 | 87.40000 | 2.0750000 | 3.1562155 |
| g__Faecisoma | 2 | 93.01500 | 1.8965000 | 1.4232745 |
| g__Faecivivens | 2 | 76.76500 | 1.5000000 | 2.4873980 |
| g__Fluviibacter | 2 | 73.96000 | 0.2360000 | 1.4886875 |
| g__Frisingicoccus | 2 | 83.62000 | 1.5335000 | 1.9329985 |
| g__Fructobacillus | 2 | 70.85000 | 1.3335000 | 1.0711470 |
| g__GCA-900066495 | 2 | 80.64500 | 4.2450000 | 2.5389705 |
| g__HGM05190 | 2 | 95.21500 | 1.8650000 | 2.7495455 |
| g__HGM13233 | 2 | 88.11000 | 1.4355000 | 1.8582025 |
| g__HGM16780 | 2 | 74.29500 | 3.8250000 | 1.1528865 |
| g__Helicobacter_D | 2 | 72.05000 | 1.0400000 | 1.2014595 |
| g__Ignatzschineria | 2 | 84.60000 | 3.3950000 | 2.2587250 |
| g__JAEDES01 | 2 | 73.47500 | 5.8150000 | 1.0426695 |
| g__JAGPHI01 | 2 | 92.36000 | 0.0800000 | 2.4903040 |
| g__JAHHTG01 | 2 | 94.32000 | 1.2100000 | 1.5924910 |
| g__JAJQBJ01 | 2 | 77.29500 | 4.7500000 | 1.8839255 |
| g__JAJQEJ01 | 2 | 80.75500 | 1.8500000 | 3.2014105 |
| g__Jeotgalibaca | 2 | 77.31500 | 3.4000000 | 2.3815695 |
| g__KLE1615 | 2 | 90.58500 | 3.8300000 | 3.4542625 |
| g__LD21 | 2 | 84.63500 | 0.6050000 | 3.6092415 |
| g__Lysinibacillus | 2 | 95.22000 | 0.0220000 | 4.2795200 |
| g__MGBC162267 | 2 | 86.14000 | 0.9600000 | 1.1269010 |
| g__Mammaliicoccus | 2 | 81.60500 | 2.0950000 | 2.2090605 |
| g__Novisyntrophococcus | 2 | 68.38000 | 2.2400000 | 1.9206375 |
| g__Onthenecus | 2 | 52.91500 | 7.1500000 | 3.0607900 |
| g__Onthousia | 2 | 69.13500 | 0.7850000 | 0.9030700 |
| g__Onthovicinus | 2 | 78.60000 | 0.1550000 | 1.9316855 |
| g__Pantoea | 2 | 75.57000 | 2.8620000 | 5.0193540 |
| g__Proteus | 2 | 99.62500 | 0.2950000 | 3.7820085 |
| g__RGIG1902 | 2 | 78.71000 | 2.0075000 | 1.6448660 |
| g__RGIG3102 | 2 | 60.67000 | 0.2600000 | 1.4511170 |
| g__RGIG3926 | 2 | 92.44500 | 0.6650000 | 1.7516480 |
| g__RGIG4790 | 2 | 93.55500 | 2.0150000 | 0.9155400 |
| g__RGIG5270 | 2 | 92.51000 | 0.2050000 | 3.4094050 |
| g__RGIG7114 | 2 | 88.96000 | 1.9265000 | 1.9151880 |
| g__RUG11788 | 2 | 94.06500 | 1.1100000 | 1.5345410 |
| g__Raoultibacter | 2 | 63.28000 | 4.4025000 | 1.7240865 |
| g__Robinsoniella | 2 | 99.51000 | 1.2525000 | 6.0692840 |
| g__Romboutsia | 2 | 65.42500 | 4.9550000 | 2.5898900 |
| g__Ruminococcus_C | 2 | 87.03000 | 1.6600000 | 2.2927460 |
| g__Shewanella | 2 | 95.18000 | 1.9850000 | 4.2699450 |
| g__Smithella | 2 | 94.25000 | 5.0250000 | 3.3927685 |
| g__TWA4 | 2 | 78.67000 | 2.5550000 | 2.8554845 |
| g__Tyzzerella | 2 | 84.23000 | 0.6750000 | 1.4449830 |
| g__UBA11358 | 2 | 86.94000 | 3.1400000 | 3.7858265 |
| g__UBA11524 | 2 | 86.84000 | 2.4685000 | 2.9045465 |
| g__UBA2475 | 2 | 85.26500 | 2.3150000 | 3.1131990 |
| g__UBA3903 | 2 | 80.10500 | 0.0835000 | 1.8982870 |
| g__UBA6265 | 2 | 74.64500 | 1.6650000 | 2.6058865 |
| g__UMGS1585 | 2 | 73.24000 | 4.1195000 | 1.8699425 |
| g__UMGS2016 | 2 | 73.07500 | 1.4840000 | 1.0016345 |
| g__UMGS2069 | 2 | 82.80500 | 1.1100000 | 0.9754800 |
| g__UMGS75 | 2 | 91.98000 | 0.8400000 | 1.5794495 |
| g__UMGS995 | 2 | 88.62000 | 2.2650000 | 1.3178675 |
| g__Vagococcus | 2 | 66.47500 | 5.3350000 | 1.8343795 |
| g__Veillonella_A | 2 | 93.89500 | 0.3450000 | 2.2712830 |
| g__WQYD01 | 2 | 63.44000 | 2.4500000 | 1.4795965 |
| g__Aerococcus | 1 | 59.02000 | 8.6300000 | 1.3373320 |
| g__Aeromicrobium | 1 | 99.89000 | 0.6400000 | 2.8213450 |
| g__Agrococcus | 1 | 98.43000 | 0.0300000 | 2.5044110 |
| g__Alangreenwoodia | 1 | 96.93000 | 0.1200000 | 3.1569430 |
| g__Albibacterium | 1 | 99.97000 | 0.3000000 | 3.7405060 |
| g__Alcaligenes | 1 | 56.61000 | 6.1300000 | 2.7206030 |
| g__Aliidiomarina | 1 | 52.20000 | 3.1400000 | 1.4865380 |
| g__Anaerocaecibacter | 1 | 78.76000 | 2.2360000 | 1.5971480 |
| g__Arachnia | 1 | 56.85000 | 0.2300000 | 1.7251140 |
| g__Bacilliculturomica | 1 | 97.00000 | 2.0950000 | 1.2819470 |
| g__Bacteroides_E | 1 | 99.43000 | 0.4500000 | 2.6663310 |
| g__Bacteroides_H | 1 | 95.02000 | 0.5660000 | 3.4673400 |
| g__Barb7 | 1 | 98.58000 | 0.6200000 | 6.1182190 |
| g__Barnesiella | 1 | 99.35000 | 0.0900000 | 3.0426880 |
| g__Borkfalkia | 1 | 78.95000 | 4.4800000 | 1.7753920 |
| g__Bradyrhizobium | 1 | 62.81000 | 1.7500000 | 5.0405010 |
| g__Brevibacterium | 1 | 65.01000 | 1.8600000 | 3.2356890 |
| g__Buchnera | 1 | 95.05000 | 0.7100000 | 0.5147370 |
| g__C7867-006 | 1 | 90.27000 | 8.1700000 | 0.7971490 |
| g__CAG-1193 | 1 | 64.91000 | 0.6700000 | 1.2539700 |
| g__CAG-170 | 1 | 85.03000 | 0.1900000 | 2.0396770 |
| g__CAG-177 | 1 | 81.87000 | 1.8200000 | 1.7078730 |
| g__CAG-217 | 1 | 52.02000 | 0.5200000 | 1.0088070 |
| g__CAG-272 | 1 | 78.92000 | 0.6900000 | 1.5878050 |
| g__CAG-313 | 1 | 69.08000 | 2.0900000 | 1.4483860 |
| g__CAG-314 | 1 | 87.89000 | 1.0700000 | 1.3074640 |
| g__CAG-433 | 1 | 92.35000 | 2.4400000 | 1.3596480 |
| g__CAG-582 | 1 | 92.69000 | 0.0000000 | 1.2631680 |
| g__CAG-793 | 1 | 89.49000 | 1.9100000 | 1.8937350 |
| g__CAIQJJ01 | 1 | 53.49000 | 2.3600000 | 3.4070360 |
| g__CAIQQL01 | 1 | 90.32000 | 0.2600000 | 1.1657700 |
| g__CAJAUT01 | 1 | 87.93000 | 7.6400000 | 0.7850580 |
| g__CAJMSU01 | 1 | 88.06000 | 1.0400000 | 1.0920350 |
| g__CAKOLD01 | 1 | 62.29000 | 0.5800000 | 0.9057680 |
| g__CAKVLS01 | 1 | 69.22000 | 0.5900000 | 0.7301980 |
| g__CALUVN01 | 1 | 84.24000 | 0.6100000 | 1.7451340 |
| g__CALVUN01 | 1 | 57.65000 | 9.6490000 | 2.3278350 |
| g__CALVXC01 | 1 | 92.39000 | 1.9100000 | 1.0055050 |
| g__CALWOS01 | 1 | 53.90000 | 1.0900000 | 1.6640440 |
| g__CALXEL01 | 1 | 79.08000 | 2.0740000 | 2.2882710 |
| g__CALXJL01 | 1 | 75.30000 | 1.7600000 | 1.1251280 |
| g__CALXUC01 | 1 | 50.60000 | 6.6430000 | 0.9825170 |
| g__CALXVS01 | 1 | 70.63000 | 1.5300000 | 1.0296420 |
| g__Caccosoma | 1 | 89.73000 | 1.6850000 | 1.2940300 |
| g__Cardinium | 1 | 84.75000 | 0.5000000 | 0.7669200 |
| g__Chiayiivirga | 1 | 92.95000 | 0.2100000 | 2.9693770 |
| g__Citrobacter_A | 1 | 97.08000 | 3.1420000 | 4.8801630 |
| g__Cloacibacillus | 1 | 99.94000 | 1.4500000 | 3.6037150 |
| g__Clostridioides | 1 | 99.30000 | 0.0000000 | 4.2129860 |
| g__Clostridium_AH | 1 | 60.75000 | 2.9200000 | 1.9427030 |
| g__Clostridium_AI | 1 | 98.11000 | 4.7700000 | 4.1531360 |
| g__Coprococcus_A | 1 | 82.82000 | 1.0800000 | 2.5061970 |
| g__DUUI01 | 1 | 97.85000 | 0.0800000 | 1.5162980 |
| g__DYRC01 | 1 | 81.39000 | 3.7300000 | 4.0181950 |
| g__Duodenibacillus | 1 | 94.85000 | 1.1100000 | 2.1803970 |
| g__Dwaynesavagella | 1 | 98.05000 | 2.0300000 | 2.1247500 |
| g__Dysgonomonas | 1 | 98.90000 | 0.5640000 | 2.5705980 |
| g__Edwardsiella | 1 | 90.83000 | 0.5200000 | 2.8654900 |
| g__Enterococcus_J | 1 | 50.72000 | 1.1700000 | 0.9908680 |
| g__Erysipelothrix | 1 | 99.95000 | 3.2900000 | 2.1357920 |
| g__FEN-1139 | 1 | 97.42000 | 7.9000000 | 11.3623140 |
| g__FEN-1279 | 1 | 99.55000 | 0.1900000 | 3.4961820 |
| g__Fermentimonas | 1 | 99.97000 | 0.1000000 | 3.9489400 |
| g__Fimiplasma | 1 | 96.94000 | 0.0500000 | 1.5553540 |
| g__Firm-04 | 1 | 67.01000 | 2.3400000 | 1.2865310 |
| g__Frigididesulfovibrio | 1 | 94.73000 | 0.0700000 | 3.0212370 |
| g__Gallibacter | 1 | 96.32000 | 0.2600000 | 1.8428150 |
| g__Geddesella | 1 | 96.73000 | 0.0300000 | 2.1005630 |
| g__Gordonia | 1 | 71.73000 | 1.6800000 | 2.9947940 |
| g__HGM10766 | 1 | 92.36000 | 0.7300000 | 1.3536230 |
| g__HGM11525 | 1 | 67.71000 | 3.4000000 | 2.5100260 |
| g__HGM12545 | 1 | 76.13000 | 3.4800000 | 2.2671200 |
| g__HGM13010 | 1 | 69.41000 | 1.5200000 | 1.8758610 |
| g__Halomonas | 1 | 54.30000 | 8.2900000 | 2.0029490 |
| g__Halopseudomonas | 1 | 72.55000 | 2.3400000 | 2.4694990 |
| g__Heteroruminococcus | 1 | 51.25000 | 0.6700000 | 1.4534730 |
| g__Holdemania | 1 | 94.52000 | 0.0000000 | 3.0449160 |
| g__Holophaga | 1 | 71.42000 | 4.6500000 | 3.2369970 |
| g__Hominisplanchenecus | 1 | 52.63000 | 9.1700000 | 2.0338570 |
| g__Hylemonella | 1 | 56.38000 | 0.4800000 | 1.2174180 |
| g__IGN3 | 1 | 94.67000 | 1.7400000 | 4.0465950 |
| g__JAAWPK01 | 1 | 79.96000 | 9.5700000 | 1.1489760 |
| g__JAAYKM01 | 1 | 93.11000 | 4.5600000 | 2.4479890 |
| g__JAAYSD01 | 1 | 97.14000 | 0.8000000 | 2.2232730 |
| g__JAAZDN01 | 1 | 81.34000 | 1.5600000 | 1.6726130 |
| g__JABFSR01 | 1 | 79.06000 | 2.8400000 | 4.0676450 |
| g__JABUSF01 | 1 | 67.08000 | 0.0500000 | 1.0973490 |
| g__JACRCG01 | 1 | 99.99000 | 1.2000000 | 3.6243310 |
| g__JACRJP01 | 1 | 64.10000 | 0.4300000 | 0.5241010 |
| g__JADLHS01 | 1 | 69.19000 | 5.2800000 | 4.5299160 |
| g__JAERTD01 | 1 | 78.85000 | 1.0800000 | 2.4014670 |
| g__JAEWLZ01 | 1 | 62.06000 | 1.9580000 | 1.0931320 |
| g__JAEZVV01 | 1 | 79.93000 | 1.0200000 | 2.0140720 |
| g__JAFAFE01 | 1 | 84.78000 | 1.4900000 | 2.4148500 |
| g__JAFGIC01 | 1 | 79.70000 | 5.2500000 | 3.5743770 |
| g__JAFGVL01 | 1 | 50.93000 | 8.6800000 | 2.5758390 |
| g__JAFTYR01 | 1 | 100.00000 | 0.6200000 | 3.0245750 |
| g__JAGNPU01 | 1 | 91.60000 | 1.4900000 | 2.7235160 |
| g__JAGOBP01 | 1 | 68.76000 | 1.3700000 | 2.5018200 |
| g__JAHHTM01 | 1 | 50.03000 | 8.9230000 | 4.3682840 |
| g__JAHHUI01 | 1 | 97.74000 | 0.6500000 | 1.5288480 |
| g__JAHZHG01 | 1 | 69.92000 | 5.7600000 | 2.6796420 |
| g__JAILHT01 | 1 | 80.35000 | 0.6900000 | 3.0262580 |
| g__JAJPXI01 | 1 | 97.85000 | 1.9500000 | 1.9234720 |
| g__JAJQAW01 | 1 | 65.82000 | 2.8700000 | 1.8167530 |
| g__JAKALQ01 | 1 | 50.86000 | 2.9100000 | 1.5432920 |
| g__JALENY01 | 1 | 81.94000 | 0.0200000 | 2.5501840 |
| g__JALRDG01 | 1 | 86.80000 | 0.3000000 | 0.7550770 |
| g__JAMLIO01 | 1 | 96.59000 | 1.3200000 | 2.4054180 |
| g__JJ008 | 1 | 100.00000 | 0.3300000 | 4.2966590 |
| g__Jeotgalicoccus | 1 | 98.56000 | 4.5100000 | 2.0592920 |
| g__Kluyvera | 1 | 99.63000 | 0.5800000 | 4.6952270 |
| g__Kosakonia | 1 | 97.88000 | 4.7600000 | 5.4786960 |
| g__Lachnoclostridium | 1 | 92.39000 | 1.3420000 | 4.1176900 |
| g__Lachnoclostridium_B | 1 | 90.38000 | 1.4610000 | 2.8312080 |
| g__Lactococcus_A | 1 | 99.74000 | 1.0900000 | 2.5777500 |
| g__Lapidilactobacillus | 1 | 100.00000 | 0.9200000 | 1.8477010 |
| g__Lentilactobacillus | 1 | 65.07000 | 3.1900000 | 1.0477630 |
| g__Leuconostoc | 1 | 74.42000 | 6.7100000 | 1.4773370 |
| g__Limnohabitans | 1 | 94.85000 | 4.9300000 | 2.3250530 |
| g__Limousia | 1 | 89.53000 | 1.3420000 | 1.6878580 |
| g__Luteolibacter | 1 | 74.78000 | 0.9600000 | 3.1301400 |
| g__MGBC102946 | 1 | 53.58000 | 0.2500000 | 0.6341430 |
| g__MGBC108787 | 1 | 88.20000 | 1.1230000 | 1.2333140 |
| g__MGBC113645 | 1 | 63.63000 | 1.0780000 | 1.8645750 |
| g__MGBC140090 | 1 | 95.54000 | 1.0200000 | 2.1087060 |
| g__MGBC143601 | 1 | 95.88000 | 0.4400000 | 1.1444400 |
| g__MGBC163016 | 1 | 67.37000 | 2.2900000 | 1.3527210 |
| g__Marinobacter | 1 | 50.85000 | 2.0600000 | 1.5248470 |
| g__Mediterraneibacter | 1 | 55.07000 | 4.0200000 | 1.3066050 |
| g__Methanobacterium_A | 1 | 96.44000 | 0.1100000 | 2.2352770 |
| g__Methanomethylophilus | 1 | 98.38000 | 0.8060000 | 1.6299110 |
| g__Methanoplasma | 1 | 95.48000 | 1.1600000 | 1.2943750 |
| g__Methanoregula | 1 | 58.96000 | 9.9300000 | 1.7568370 |
| g__Methanosphaera | 1 | 91.34000 | 0.2000000 | 1.5985010 |
| g__Methanothrix | 1 | 96.26000 | 0.3900000 | 2.3085830 |
| g__Methyloglobulus | 1 | 66.74000 | 2.0400000 | 2.2778330 |
| g__Mycetocola | 1 | 93.00000 | 4.1700000 | 3.4344310 |
| g__NC2004 | 1 | 53.18000 | 3.3800000 | 1.6265820 |
| g__NIC37A-2 | 1 | 55.66000 | 0.1600000 | 2.5307600 |
| g__OLB17 | 1 | 89.84000 | 1.5100000 | 3.9879030 |
| g__Oligella | 1 | 99.74000 | 3.5500000 | 2.2122110 |
| g__Onthoplasma | 1 | 97.69000 | 0.2100000 | 1.1555950 |
| g__Ornithomonoglobus | 1 | 82.73000 | 0.6700000 | 1.7929430 |
| g__Ornithomonoglobus_A | 1 | 51.34000 | 7.2500000 | 1.7475840 |
| g__Oxalobacter | 1 | 99.94000 | 0.1900000 | 2.5254150 |
| g__Paenibacillus | 1 | 98.92000 | 0.0000000 | 3.8814710 |
| g__Paludibacter | 1 | 100.00000 | 3.2200000 | 4.5095440 |
| g__Paratractidigestivibacter | 1 | 68.21000 | 0.6600000 | 1.3958120 |
| g__PeH17 | 1 | 96.56000 | 0.2600000 | 1.7954600 |
| g__Proteiniphilum | 1 | 99.96000 | 0.5500000 | 2.9177370 |
| g__Providencia | 1 | 91.23000 | 2.5800000 | 4.2267620 |
| g__Pseudochrobactrum | 1 | 51.22000 | 4.7400000 | 1.9998690 |
| g__Pseudocitrobacter | 1 | 96.28000 | 8.7140000 | 4.8484100 |
| g__Pseudomonas | 1 | 76.97000 | 0.2750000 | 4.2230230 |
| g__Pusillimonas_B | 1 | 99.99000 | 0.6700000 | 3.9399620 |
| g__RACS-047 | 1 | 65.45000 | 1.4300000 | 1.5278680 |
| g__RFTN01 | 1 | 81.02000 | 0.9200000 | 0.7832210 |
| g__RGIG2774 | 1 | 99.33000 | 0.1700000 | 2.0010970 |
| g__RGIG3091 | 1 | 92.13000 | 1.6850000 | 1.2119560 |
| g__RGIG3701 | 1 | 93.11000 | 1.7300000 | 4.3173220 |
| g__RGIG4074 | 1 | 81.92000 | 0.8060000 | 1.6084430 |
| g__RGIG4097 | 1 | 94.96000 | 0.0200000 | 1.5882000 |
| g__RGIG423 | 1 | 53.64000 | 0.7380000 | 1.1266110 |
| g__RGIG5057 | 1 | 94.78000 | 0.1200000 | 1.3024720 |
| g__RGIG7389 | 1 | 71.24000 | 3.2900000 | 2.0355290 |
| g__RGIG8607 | 1 | 84.23000 | 1.5800000 | 2.8970540 |
| g__RPPU01 | 1 | 92.58000 | 2.0000000 | 4.3118760 |
| g__RUG11130 | 1 | 91.69000 | 0.2300000 | 2.1081430 |
| g__RUG11198 | 1 | 63.63000 | 9.1520000 | 1.7405860 |
| g__RUG11890 | 1 | 79.65000 | 1.6800000 | 1.0271300 |
| g__RUG12438 | 1 | 91.36000 | 2.6900000 | 1.2015840 |
| g__RUG12867 | 1 | 84.80000 | 1.2350000 | 1.3100890 |
| g__RUG14305 | 1 | 55.47000 | 8.9500000 | 2.9488890 |
| g__RUG14891 | 1 | 54.46000 | 8.7550000 | 3.7555800 |
| g__RUG591 | 1 | 92.44000 | 2.0900000 | 1.5980810 |
| g__Rhodoferax_C | 1 | 98.54000 | 2.8300000 | 5.2482630 |
| g__Romboutsia_D | 1 | 72.82000 | 5.5700000 | 2.3550210 |
| g__Ruania | 1 | 92.31000 | 2.5000000 | 4.2623200 |
| g__SIG230 | 1 | 85.17000 | 0.4000000 | 1.8732640 |
| g__SIG308 | 1 | 95.87000 | 1.8300000 | 3.4201330 |
| g__SIG603 | 1 | 65.91000 | 1.0060000 | 1.8239100 |
| g__SKHV01 | 1 | 98.80000 | 1.0200000 | 5.6958050 |
| g__Scatomorpha | 1 | 58.59000 | 2.4600000 | 1.4164590 |
| g__Scatosoma | 1 | 52.43000 | 0.0300000 | 0.9484970 |
| g__Schmidhempelia | 1 | 99.97000 | 0.0400000 | 1.7264330 |
| g__Schwartzia | 1 | 52.37000 | 0.1700000 | 0.7808460 |
| g__Scybalousia | 1 | 95.84000 | 1.3400000 | 1.3365280 |
| g__Serratia_A | 1 | 100.00000 | 1.3400000 | 5.8208240 |
| g__Slackia_A | 1 | 63.54000 | 0.4800000 | 1.1501420 |
| g__Stenotrophomonas | 1 | 87.83000 | 0.6350000 | 3.6664510 |
| g__Stutzerimonas | 1 | 55.33000 | 5.6800000 | 2.0687660 |
| g__Symbiothrix | 1 | 95.27000 | 0.1700000 | 2.5798760 |
| g__Syntrophorhabdus | 1 | 81.00000 | 5.4100000 | 2.3275200 |
| g__Taishania | 1 | 81.78000 | 2.0400000 | 2.7747980 |
| g__Terracidiphilus | 1 | 81.62000 | 1.9100000 | 4.2092490 |
| g__Thiodictyon | 1 | 51.80000 | 1.7500000 | 2.7653580 |
| g__Thiopseudomonas | 1 | 99.45000 | 3.0200000 | 2.7944710 |
| g__UBA10108 | 1 | 83.73000 | 2.2300000 | 0.8763760 |
| g__UBA11452 | 1 | 55.89000 | 2.6900000 | 3.2786740 |
| g__UBA1394 | 1 | 50.00000 | 9.0400000 | 3.0054700 |
| g__UBA1405 | 1 | 50.63000 | 0.3100000 | 1.7731710 |
| g__UBA1752 | 1 | 75.44000 | 1.6200000 | 1.3302750 |
| g__UBA2192 | 1 | 58.89000 | 1.3700000 | 1.2361280 |
| g__UBA2664 | 1 | 97.46000 | 0.4600000 | 3.4316890 |
| g__UBA2813 | 1 | 82.64000 | 1.9900000 | 1.6820780 |
| g__UBA2883 | 1 | 80.37000 | 2.0600000 | 1.6062150 |
| g__UBA3305 | 1 | 50.33000 | 8.1400000 | 1.6613950 |
| g__UBA3789 | 1 | 93.82000 | 5.1200000 | 1.6781770 |
| g__UBA3961 | 1 | 97.88000 | 1.3800000 | 3.6846550 |
| g__UBA4636 | 1 | 59.95000 | 0.0000000 | 1.0069370 |
| g__UBA6345 | 1 | 93.11000 | 0.2680000 | 1.2527190 |
| g__UBA710 | 1 | 98.31000 | 0.7700000 | 0.7858270 |
| g__UBA738 | 1 | 67.50000 | 0.1100000 | 1.1998320 |
| g__UBA7405 | 1 | 78.78000 | 2.2400000 | 3.7474390 |
| g__UBA9973 | 1 | 100.00000 | 0.4100000 | 0.6731830 |
| g__UMGS1124 | 1 | 86.95000 | 1.2100000 | 1.2401560 |
| g__UMGS1271 | 1 | 81.36000 | 0.3000000 | 1.0862590 |
| g__UMGS1696 | 1 | 96.30000 | 0.0200000 | 2.5538520 |
| g__UMGS1766 | 1 | 71.53000 | 1.4540000 | 2.1316140 |
| g__UMGS1781 | 1 | 100.00000 | 3.1600000 | 1.6879910 |
| g__UMGS1994 | 1 | 57.91000 | 0.5100000 | 0.7209690 |
| g__UMGS363 | 1 | 91.75000 | 0.0800000 | 2.6035780 |
| g__UMGS687 | 1 | 69.42000 | 0.8060000 | 0.7448230 |
| g__UMGS946 | 1 | 88.78000 | 0.8060000 | 1.8872360 |
| g__UMGS973 | 1 | 86.09000 | 1.9300000 | 1.5602950 |
| g__Vitreimonas | 1 | 57.65000 | 1.1400000 | 1.7915160 |
| g__Wohlfahrtiimonas | 1 | 97.13000 | 1.7300000 | 2.0760790 |
| g__Wolbachia | 1 | 98.71000 | 0.0000000 | 1.3209310 |
| g__Zhenhengia | 1 | 98.22000 | 0.6300000 | 3.4406380 |
5.4 New taxa discovery
#species
genome_metadata %>%
mutate(novelty = if_else(species == "s__", "new", "known")) %>%
group_by(novelty) %>%
summarise(
total_genomes = n(),
percentage = (total_genomes / nrow(genome_metadata)) * 100
) %>%
tt()| novelty | total_genomes | percentage |
|---|---|---|
| known | 1667 | 12.05089 |
| new | 12166 | 87.94911 |
#genus
genome_metadata %>%
mutate(novelty = if_else(genus == "g__", "new", "known")) %>%
group_by(novelty) %>%
summarise(
total_genomes = n(),
percentage = (total_genomes / nrow(genome_metadata)) * 100
) %>%
tt()| novelty | total_genomes | percentage |
|---|---|---|
| known | 11616 | 83.97311 |
| new | 2217 | 16.02689 |
#order
genome_metadata %>%
mutate(novelty = if_else(order == "o__", "new", "known")) %>%
group_by(novelty) %>%
summarise(
total_genomes = n(),
percentage = (total_genomes / nrow(genome_metadata)) * 100
) %>%
tt()| novelty | total_genomes | percentage |
|---|---|---|
| known | 13824 | 99.93493819 |
| new | 9 | 0.06506181 |
#species
genome_metadata %>%
left_join(assembly_metadata,by="assembly_id") %>%
left_join(summary_table,by="rawdata_id") %>%
mutate(novelty = if_else(species == "s__", "new", "known")) %>%
group_by(host_species) %>%
summarise(
total_genomes = n(),
new_genomes = sum(novelty == "new"),
percentage_new = (new_genomes / total_genomes) * 100
) %>%
arrange(desc(percentage_new)) %>%
tt()| host_species | total_genomes | new_genomes | percentage_new |
|---|---|---|---|
| Podarcis muralis | 2670 | 2604 | 97.52809 |
| Podarcis gaigeae | 1280 | 1246 | 97.34375 |
| Podarcis milensis | 590 | 570 | 96.61017 |
| Lissotriton helveticus | 1590 | 1526 | 95.97484 |
| Sciurus carolinensis | 1686 | 1616 | 95.84816 |
| Calotriton asper | 745 | 708 | 95.03356 |
| Podarcis pityusensis | 1046 | 974 | 93.11663 |
| Podarcis liolepis | 232 | 214 | 92.24138 |
| Podarcis filfolensis | 693 | 637 | 91.91919 |
| Trichosurus vulpecula | 61 | 54 | 88.52459 |
| Lepus europaeus | 832 | 711 | 85.45673 |
| Sciurus vulgaris | 1033 | 747 | 72.31365 |
| Psittacula echo | 123 | 66 | 53.65854 |
| Canis familiaris | 1252 | 493 | 39.37700 |
5.5 Genus - host heatmap
genus_host <- genome_metadata %>%
left_join(assembly_metadata,by="assembly_id") %>%
left_join(summary_table,by="rawdata_id") %>%
select(phylum,genus,host_species) %>%
filter(genus != "g__") %>%
group_by(phylum,genus,host_species) %>%
summarise(genomes=n()) %>%
arrange(-genomes) %>%
ungroup()
genus_host_spread <- genus_host %>%
group_by(phylum,genus) %>%
summarise(host_species=n()) %>%
arrange(-host_species)gtdb_tree <- read_tree("data/bac120_r214.tree")
gtdb_metadata <- read_tsv("data/bac120_taxonomy_r214.tsv.gz", col_names = FALSE) %>%
rename(genome=1,classification=2) %>%
separate(classification, c("domain","phylum","class","order","family","genus","species"), sep =";")
represented_genera <- gtdb_metadata %>%
filter(genus %in% genus_host$genus) %>%
filter(genome %in% gtdb_tree$tip.label) %>%
group_by(genus) %>%
slice_sample(n = 1) %>%
ungroup()
ehi_mags_tree <- keep.tip(gtdb_tree, tip=represented_genera$genome)
ehi_mags_tree$tip.label <- represented_genera %>%
filter(genome %in% ehi_mags_tree$tip.label) %>% # Keep only rows corresponding to tree tip labels
arrange(match(genome, ehi_mags_tree$tip.label)) %>% # Match order of genomes to tree tip labels
pull(genus)genus_host2 <- genus_host %>%
select(-phylum) %>%
pivot_wider(names_from = host_species, values_from = genomes) %>%
column_to_rownames(var="genus")
genus_host %>%
left_join(host_metadata,by="host_species") %>%
mutate(genus=factor(genus,levels=ehi_mags_tree$tip.label)) %>%
ggplot(aes(x=host_species,y=genus,fill=genomes)) +
facet_nested(. ~ host_class, space="free",scales="free") +
geom_tile() +
scale_fill_gradient(low = "grey", high = "#2a94d1", na.value="white") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))read_tsv("https://raw.githubusercontent.com/earthhologenome/EHI_taxonomy_colour/main/ehi_phylum_colors.tsv") %>%
right_join(genus_host, by=join_by(phylum == phylum)) %>%
select(genus,phylum) %>%
unique %>%
mutate(genus=factor(genus,levels=ehi_mags_tree$tip.label)) %>%
mutate(xaxis=NA) %>%
ggplot(aes(x=xaxis,y=genus,fill=phylum)) +
geom_tile() +
scale_fill_manual(values=phylum_colors)